Just put the two JProgressBars to a JPanel say centerPanel with BridLayout(0, 1, 5, 5).
And put the 2 JButtons START and STOP to another JPanel say buttonPanel with Layout i.e. FlowLayout(FlowLayout.LEFT, 5, 5) (This will align the JButton START with the left side of the JProgressBars, though if you want the JButtons to come somewhere in the middle of the same, then simply don't use setLayout(FlowLayout.LEFT, 5, 5). The default Layout for the JPanel will do).
Now add centerPanel to the JFrame using
frameReference.add(centerPanel, BorderLayout.CENTER)
and add buttonPanel using
frameReference.add(buttonPanel, BorderLayout.PAGE_END)
That will do :-)
EDIT 1 :
use a Border for this thingy. Like
centerPanel.setBorder(BorderFactory.createLineBorder(Color.BLACK))
That will create a Box around the centerPanel. Please have a look at this answer, though I am using TitledBorder in this example.